PDHR - ECOLI - GREMLIN Contacts

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PDHR - Pyruvate dehydrogenase complex repressor

UniProt:	P0ACL9	Sequences: MAYSKIRQPKLSDVIEQQLEFLILEGTLRPGEKLPPERELAKQFDVSRPSLREAIQRLEAKGLLLRRQGGGTFVQSSLWQSFSDPLVELLSDHPESQYDLLETRHALEGIAAYYAALRSTDEDKERIRELHHAIELAQQSGDLDAESNAVLQYQIAVTEAAHNVVLLHLLRCMEPMLAQNVRQNFELLYSRREMLPLVSSHRTRIFEAIMAGKPEEAREASHRHLAFIEEILLDRSREESRRERSLRRLEQRKN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11088
Length:	254 (206)
Sequences:	23353 (17030)
Seq/√Len:	1186.5

ECOLI - PDHR GLCC EXUR UXUR LLDR NANR YDFH YIEP YJJM DGOR MCBR CSIR FADR FRLR YEGW YIDP PHNF
BACSU - GNTR YDHC YCBG LUTR YVOA YMFC YURK TRER YYDK
SULSO - Q97YR4

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
128_R	210_M	3.862	1.00
113_Y	218_R	3.326	1.00
213_K	216_E	2.933	1.00
135_E	203_T	2.872	1.00
29_R	32_E	2.758	1.00
22_L	27_T	2.721	1.00
22_L	43_Q	2.389	1.00
106_A	110_I	2.320	1.00
37_E	48_R	2.251	1.00
99_D	164_V	2.230	1.00
126_R	156_A	2.197	1.00
105_H	226_A	2.109	1.00
16_E	57_R	2.092	1.00
65_L	75_Q	2.033	1.00
20_E	61_K	1.999	1.00
117_L	214_P	1.958	1.00
15_I	46_V	1.947	1.00
102_E	114_Y	1.912	1.00
124_K	210_M	1.833	1.00
123_D	162_H	1.811	1.00
208_A	216_E	1.795	1.00
15_I	44_F	1.788	1.00
120_T	123_D	1.776	1.00
159_E	167_L	1.761	1.00
66_R	72_T	1.738	1.00
156_A	159_E	1.719	1.00
142_D	145_A	1.705	1.00
131_H	206_F	1.676	1.00
18_Q	22_L	1.649	1.00
109_G	222_H	1.646	1.00
201_H	227_F	1.619	1.00
113_Y	214_P	1.606	1.00
216_E	220_A	1.588	1.00
154_Q	202_R	1.578	1.00
9_P	17_Q	1.571	1.00
103_T	169_L	1.569	1.00
21_F	25_E	1.556	1.00
109_G	218_R	1.553	1.00
218_R	222_H	1.547	1.00
110_I	113_Y	1.517	1.00
204_R	220_A	1.472	1.00
67_R	70_G	1.468	1.00
207_E	211_A	1.443	1.00
158_T	170_L	1.437	1.00
155_I	171_R	1.419	1.00
130_L	149_A	1.414	1.00
133_A	149_A	1.411	1.00
112_A	217_A	1.405	1.00
123_D	160_A	1.401	1.00
16_E	61_K	1.396	1.00
168_H	172_C	1.391	1.00
128_R	206_F	1.389	1.00
165_V	176_M	1.383	1.00
105_H	222_H	1.381	1.00
211_A	216_E	1.361	1.00
135_E	199_S	1.352	1.00
38_R	42_K	1.344	1.00
105_H	229_E	1.344	1.00
203_T	207_E	1.324	1.00
99_D	165_V	1.312	1.00
128_R	132_H	1.274	1.00
214_P	218_R	1.272	1.00
133_A	152_Q	1.266	1.00
39_E	43_Q	1.259	1.00
119_S	124_K	1.252	1.00
131_H	203_T	1.238	1.00
129_E	133_A	1.235	1.00
219_E	223_R	1.204	1.00
201_H	224_H	1.198	1.00
33_K	73_F	1.196	1.00
40_L	51_L	1.195	1.00
105_H	109_G	1.193	1.00
98_Y	233_L	1.189	1.00
18_Q	21_F	1.187	1.00
14_V	18_Q	1.185	1.00
130_L	156_A	1.184	1.00
67_R	73_F	1.169	1.00
22_L	44_F	1.161	1.00
216_E	219_E	1.156	1.00
18_Q	44_F	1.153	1.00
104_R	108_E	1.150	1.00
113_Y	215_E	1.142	1.00
98_Y	229_E	1.136	1.00
155_I	159_E	1.129	1.00
119_S	160_A	1.127	1.00
152_Q	156_A	1.120	1.00
112_A	116_A	1.119	1.00
222_H	226_A	1.118	1.00
119_S	212_G	1.113	1.00
124_K	206_F	1.112	1.00
119_S	123_D	1.110	1.00
145_A	148_N	1.108	1.00
157_V	209_I	1.107	1.00
150_V	154_Q	1.106	1.00
109_G	113_Y	1.102	1.00
59_E	66_R	1.099	1.00
207_E	210_M	1.098	1.00
28_L	74_V	1.088	1.00
112_A	221_S	1.087	1.00
99_D	163_N	1.084	1.00
206_F	210_M	1.060	1.00
131_H	134_I	1.057	1.00
126_R	159_E	1.050	1.00
102_E	163_N	1.041	1.00
128_R	203_T	1.039	1.00
131_H	135_E	1.038	1.00
111_A	158_T	1.032	1.00
130_L	152_Q	1.029	1.00
132_H	135_E	1.024	1.00
156_A	160_A	1.024	1.00
154_Q	224_H	1.020	1.00
59_E	64_L	1.019	1.00
229_E	233_L	1.015	1.00
124_K	212_G	1.014	1.00
202_R	224_H	1.014	1.00
126_R	129_E	0.990	1.00
149_A	152_Q	0.990	1.00
161_A	167_L	0.985	1.00
65_L	73_F	0.984	1.00
116_A	214_P	0.982	1.00
53_E	56_Q	0.979	1.00
169_L	172_C	0.967	1.00
204_R	223_R	0.965	1.00
200_S	204_R	0.964	1.00
208_A	213_K	0.963	1.00
108_E	154_Q	0.963	1.00
37_E	52_R	0.962	1.00
110_I	218_R	0.957	1.00
9_P	14_V	0.955	1.00
22_L	28_L	0.950	1.00
204_R	216_E	0.946	1.00
114_Y	118_R	0.944	1.00
148_N	152_Q	0.938	1.00
153_Y	206_F	0.935	1.00
125_E	129_E	0.927	1.00
55_I	72_T	0.926	1.00
116_A	209_I	0.920	1.00
23_I	74_V	0.917	1.00
64_L	72_T	0.917	1.00
205_I	221_S	0.914	1.00
12_S	57_R	0.906	1.00
126_R	130_L	0.905	1.00
36_P	39_E	0.897	1.00
124_K	128_R	0.897	1.00
67_R	71_G	0.897	1.00
204_R	207_E	0.894	1.00
104_R	225_L	0.883	1.00
130_L	133_A	0.881	1.00
96_S	165_V	0.880	1.00
33_K	71_G	0.880	1.00
103_T	165_V	0.875	1.00
41_A	51_L	0.875	1.00
95_E	99_D	0.875	1.00
215_E	219_E	0.872	1.00
70_G	73_F	0.866	1.00
57_R	60_A	0.862	1.00
135_E	139_Q	0.858	1.00
150_V	202_R	0.854	1.00
215_E	218_R	0.852	1.00
118_R	162_H	0.850	1.00
20_E	63_L	0.849	1.00
110_I	114_Y	0.844	1.00
167_L	171_R	0.841	1.00
128_R	207_E	0.839	1.00
16_E	20_E	0.839	1.00
39_E	42_K	0.837	1.00
95_E	162_H	0.835	1.00
123_D	126_R	0.831	1.00
137_A	145_A	0.826	1.00
127_I	156_A	0.826	1.00
199_S	203_T	0.826	1.00
136_L	140_S	0.822	1.00
133_A	136_L	0.820	1.00
47_S	50_S	0.819	1.00
119_S	209_I	0.817	1.00
116_A	212_G	0.815	1.00
40_L	55_I	0.801	1.00
20_E	24_L	0.800	1.00
121_D	212_G	0.799	1.00
56_Q	59_E	0.798	1.00
132_H	136_L	0.797	1.00
11_L	14_V	0.796	1.00
116_A	217_A	0.796	1.00
55_I	64_L	0.794	1.00
121_D	125_E	0.793	1.00
127_I	206_F	0.791	1.00
205_I	220_A	0.791	1.00
134_I	146_E	0.789	1.00
204_R	208_A	0.780	1.00
196_P	200_S	0.778	1.00
115_A	160_A	0.777	1.00
13_D	57_R	0.773	1.00
46_V	51_L	0.770	1.00
132_H	203_T	0.767	1.00
208_A	220_A	0.764	1.00
165_V	169_L	0.763	1.00
11_L	50_S	0.761	1.00
226_A	230_E	0.746	1.00
113_Y	117_L	0.745	1.00
102_E	229_E	0.745	1.00
155_I	174_E	0.744	1.00
12_S	16_E	0.742	1.00
10_K	13_D	0.740	1.00
115_A	119_S	0.739	1.00
114_Y	117_L	0.739	1.00
165_V	168_H	0.729	1.00
102_E	118_R	0.726	1.00
126_R	152_Q	0.723	1.00
101_L	228_I	0.719	1.00
103_T	166_L	0.718	1.00
114_Y	163_N	0.716	1.00
220_A	223_R	0.712	1.00
56_Q	66_R	0.710	1.00
27_T	43_Q	0.709	1.00
133_A	145_A	0.704	1.00
219_E	222_H	0.703	1.00
151_L	178_A	0.697	1.00
124_K	209_I	0.696	1.00
145_A	149_A	0.696	1.00
125_E	210_M	0.693	1.00
205_I	217_A	0.688	1.00
125_E	128_R	0.681	1.00
103_T	111_A	0.679	1.00
129_E	132_H	0.671	1.00
137_A	149_A	0.663	1.00
226_A	229_E	0.663	1.00
131_H	199_S	0.662	1.00
123_D	159_E	0.660	1.00
223_R	227_F	0.659	1.00
227_F	231_I	0.656	1.00
155_I	167_L	0.654	1.00
205_I	224_H	0.654	1.00
57_R	61_K	0.649	1.00
105_H	225_L	0.642	1.00
9_P	13_D	0.641	1.00
96_S	164_V	0.637	1.00
133_A	137_A	0.634	1.00
69_G	72_T	0.628	1.00
50_S	54_A	0.627	1.00
78_L	96_S	0.624	1.00
112_A	214_P	0.620	1.00
28_L	32_E	0.619	1.00
111_A	161_A	0.615	1.00
123_D	156_A	0.613	1.00
102_E	110_I	0.613	1.00
151_L	174_E	0.613	1.00
201_H	204_R	0.611	1.00
103_T	107_L	0.603	1.00
106_A	166_L	0.602	1.00
115_A	161_A	0.601	1.00
146_E	198_V	0.596	1.00
115_A	157_V	0.589	1.00
22_L	26_G	0.587	1.00
108_E	202_R	0.586	1.00
137_A	142_D	0.585	1.00
152_Q	155_I	0.583	1.00
109_G	214_P	0.582	1.00
38_R	41_A	0.578	1.00
230_E	234_D	0.576	1.00
136_L	139_Q	0.575	1.00
134_I	199_S	0.571	1.00
109_G	221_S	0.570	1.00
12_S	53_E	0.566	1.00
30_P	76_S	0.566	1.00
44_F	51_L	0.561	1.00
106_A	109_G	0.559	1.00
34_L	64_L	0.558	1.00
107_L	170_L	0.557	1.00
127_I	160_A	0.554	1.00
122_E	126_R	0.554	1.00
95_E	164_V	0.553	1.00
111_A	166_L	0.551	1.00
73_F	76_S	0.547	1.00
94_P	98_Y	0.543	1.00
31_G	76_S	0.543	1.00
56_Q	60_A	0.542	1.00
230_E	233_L	0.541	1.00
194_M	197_L	0.539	1.00
121_D	124_K	0.536	1.00
168_H	176_M	0.535	1.00
223_R	226_A	0.531	1.00
121_D	210_M	0.528	1.00
113_Y	222_H	0.528	1.00
28_L	34_L	0.527	1.00
137_A	141_G	0.525	1.00
19_L	40_L	0.525	1.00
112_A	157_V	0.524	1.00
158_T	174_E	0.522	1.00
95_E	98_Y	0.521	1.00
75_Q	179_Q	0.520	1.00
42_K	45_D	0.519	1.00
108_E	225_L	0.517	1.00
217_A	221_S	0.517	1.00
127_I	131_H	0.516	1.00
200_S	203_T	0.514	1.00
205_I	208_A	0.513	1.00
194_M	231_I	0.513	1.00
24_L	63_L	0.512	1.00
135_E	200_S	0.510	1.00
168_H	171_R	0.509	1.00
110_I	166_L	0.508	1.00
193_E	196_P	0.507	1.00
221_S	225_L	0.505	1.00
28_L	43_Q	0.505	1.00
227_F	230_E	0.504	1.00
114_Y	161_A	0.503	1.00
22_L	25_E	0.502	1.00
139_Q	196_P	0.501	1.00
116_A	218_R	0.500	1.00

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
3sxyA	2	0.7874	100	0.195	Contact Map
4p96A	2	0.9449	100	0.2	Contact Map
3c7jA	4	0.8701	100	0.201	Contact Map
2hs5A	1	0.815	100	0.205	Contact Map
2di3A	2	0.8937	100	0.207	Contact Map
3ihuA	1	0.8031	100	0.213	Contact Map
4p9fA	1	0.8307	100	0.215	Contact Map
1hw1A	2	0.874	100	0.244	Contact Map
4r1hA	2	0.4488	99.9	0.551	Contact Map
3ic7A	2	0.437	99.9	0.552	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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